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SJTU-CGM / HUPAN

Human pan-genome analysis pipeline
http://cgm.sjtu.edu.cn/hupan/
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‘getUnalnCtg’ function has some new problem #5

Closed chenshixuan closed 4 years ago

chenshixuan commented 4 years ago

When Use HUPAN with the command "/HUPAN/bin/hupan getUnalnCtg -p contig /Hupan/02test/02step2_extracseq/candidate/data/ Hupan/02test/03step3/quast_result/data/ Unalign_result" ,the error messge is "Error04: cannot open data directory: /Hupan/02test/03step3/quast_result/data/sample1/contigs_reports/nucmer_output/" .Actually,the output directory's name is "minimap_output" ,not the "nucmer_output". However, the program is still runnin with the command "hupan getUnalnCtg",the two output result directories are "quast_result , Unalign_result".The "quast_result" is same to the commmad "hupan assemSta" output result,So why this step is same to the last step ?Compute twice! Now the Unalign_result still empty. Thank you very much!

zhqduan commented 4 years ago

As you described, this error is caused by the higher version of QUAST you used. In QUAST 5.0 or higher, the new fast aligner software 'minimap2' is used (http://quast.sourceforge.net/quast-lg.html). However, HUPAN is designed for results from nucmer. Please use QUAST 4.5

chenshixuan commented 4 years ago

OK，thank you very much